Billy was surprised to be summoned to the captain's cabin, but had no idea that he might be in trouble. In fact, he thought the captain might be promoting him to the position of his coxswain. When he arrives and he, Captain Vere, and Claggart were alone in the cabin, though, Claggart repeated his accusation against Billy.
Billy is so assured of his good standing on the ship and of his own loyal behavior that he thinks he is going to be promoted. Claggart repeats his untrue accusations. (Though, again, one might ask why Claggart would bring absolutely unsubstantiated claims against Billy to Vere if he didn't believe them? Did he truly hope to convince Vere without any evidence? Would simple malice against Billy be worth the risk of such an action?)
Billy went pale at hearing the accusation and was so shocked he couldn't speak. Captain Vere told him to speak and defend himself, but Billy was so surprised by the accusation that he could produce nothing but "strange dumb gesturing and gurgling."
To someone unfamiliar with Billy's character and speech problem, his behavior might appear to be that of a guilty man.
Captain Vere had known a young schoolmate who suffered from a speech impediment similar to Billy's, so he recognized Billy's inability to speak as mere nervousness, rather than a sign of guilt. He encouraged Billy to take his time in replying. Billy tried to say something but still couldn't, and suddenly "his right arm shot out," hitting Claggart, who fell to the floor.
Vere is able to recognize that Billy's inability to speak is not a sign of guilt. The implication is that Billy, unable to communicate because of his stutter, is unable to stop him from responding in some way, and so he does so violently, at odds with his normally gentle nature.
Captain Vere was stunned, and his former fatherly demeanor toward Billy was "replaced by the military disciplinarian." He ordered Billy to go to another room and wait there and then sent another sailor to bring the ship's surgeon to his cabin. The surgeon arrived and pronounced Claggart to be dead.
Captain Vere immediately puts aside his personal fondness for Billy and assumes his role within the naval community, as a military commander.
Captain Vere was overcome with emotion and cried out that Claggart was "struck dead by an angel of God! Yet the angel must hang!" The captain gathered himself and told the surgeon what had happened. After moving Claggart's body to a compartment, he ordered the surgeon to bring the ship's lieutenants and captain of marines to him in order to form a drumhead court.
Even as Billy has just killed someone, Captain Vere insists on his angelic nature. The fact that an "angel" must be hanged encapsulates the difficult decision of how to mete out justice in this case, in which someone who Vere believes to be innocent has committed accidental murder. This question will preoccupy Vere and his court in the following chapters.